Useful Links and Proteomics Resources
Mass Calculators (Mongo) website - This website is useful for calculating theoretical masses for nucleic acids, proteins, and other molecules.
http://library.med.utah.edu/masspec
Matrix Science (Mascot) – web site for Mascot database searches. Useful information about how the databases searches are done and help with interpretation and understanding database search results.
http://www.matrixscience.com/
http://www.matrixscience.com/help/results_help.html (help with the Mascot report)
http://www.matrixscience.com/help/scoring_help.html (help understanding scoring)
http://www.matrixscience.com/help/interpretation_help.html (help with results interpretation)
Expasy – a web site with many useful protein tools and links
http://ca.expasy.org/
Protein Prospector – a web site from UCSF with useful protein search tools and links
http://prospector.ucsf.edu/
ABRF – a web site for shared proteomics information
http://www.abrf.org/
Delta Mass (ABRF) – a useful web site for identification of protein and peptide modifications based on net mass change observed in mass spectra.
http://www.abrf.org/index.cfm/dm.home
Collaboratory for MS3D – a web site from Sandia Labs that has useful software for searching mass spec data for disulfide linkages or other crosslinks.
http://www.ms3d.org/ http://www.ms3d.org/links.php http://roswell.ca.sandia.gov/~mmyoung/
OMMSA – a free on-line web site for protein database searching of MS/MS data.
http://pubchem.ncbi.nlm.nih.gov/omssa
ISB (Institute for Systems Biology) proteomics tools
Fred Hutchinson Cancer Center
http://proteomics.fhcrc.org/CPL/home.html
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